Thank Peter! How do I make the title in bold font?
John
- Original Message
From: Peter Ehlers
To: array chip
Cc: R
Sent: Tue, June 28, 2011 10:52:07 AM
Subject: Re: [R] how to print "<=" in plot title
On 2011-06-28 10:25, array chip wrote:
> Hi, how can I print
(from
variable x) in bold. Anyway to solve that?
Thanks again!
John
- Original Message
From: David Winsemius
To: Peter Ehlers
Cc: array chip ; R
Sent: Tue, June 28, 2011 11:04:07 AM
Subject: Re: [R] how to print "<=" in plot title
On Jun 28, 2011, at 1:52 PM, Peter E
David,
I tried your suggestion, still not working:
x<-3
plot(1:10)
title(bquote(bold(x) <= bold(as.character(.(x)) )))
It prints x<=as.character(3) as title
Thanks
John
- Original Message
From: David Winsemius
To: array chip
Cc: Peter Ehlers ; R
Sent: Tue, June 28, 2
Thank you Alan again! Hope you could also share your thought on my another
email about the coding of censoring before death..
Thanks again!
John
- Original Message
From: alanm (Alan Mitchell)
To: array chip ; David Winsemius
Cc: r-help@r-project.org
Sent: Tue, June 28, 2011 11
Thank you David for the obvious fix and sorry for my lacking innovative spirit,
:-)
Really, I know I haven't grasped the essence of plotting these math symbols in
R.
John
- Original Message
From: David Winsemius
To: array chip
Cc: Peter Ehlers ; R
Sent: Tue, June 28, 2011
Thank you again David for the thoughtful comments on plotmath. Really
appreciated.
John
- Original Message
From: David Winsemius
To: array chip
Cc: Peter Ehlers ; R
Sent: Tue, June 28, 2011 12:20:49 PM
Subject: Re: [R] how to print "<=" in plot title
On Jun 28, 201
ce or recurrence-free survival) with death as
being censored. Because death is a competing risk for recurrence, does this
mean
those KM curves are not appropriate, instead CI curves should be used?
Thanks very much!
John
- Original Message
From: Terry Therneau
To: array chip
Cc: r-h
Hi, does anyone know how to make decimal points midline when plotting? The
journal to which we are going to submit a manuscript require this particular
formatting, and it gives direction how to do this on PC: hold down ALT key and
type 0183 on the number pad
Thanks
John
[[alternative H
Thanks Uwe, options(OutDec="\xB7") worked!
From: Uwe Ligges
To: John Kane
roject.org>
Sent: Wednesday, August 8, 2012 12:43 PM
Subject: Re: [R] decimal points midline
On 08.08.2012 21:22, John Kane wrote:
> Can you point to an example? It sounds like the
Hi, I am trying forestplot() and metaplot() from rmeta package to plot some
hazard ratios. Now foreatplot() can draw clipping with "<" or ">" at the ends
of the confidence line using "clip" argument, but can't use multiple colors for
different lines. On the other hand, metaplot() can use differe
Hi, I have a seemingly simple proportional test. here is the question I am
trying to answer:
There is a test running each day in the lab, the test comes out as
either positive or negative. So at the end of each month, we can calculate a
positive rate in that month as the proportion of positive
Hi all, I asked this yesterday, but hadn't got any response yet. Understand
this is not pure R technical question, but more of statistical. With many
statistical experts in the list, I would appreciate any suggestions...
Many thanks
John
--
Hi,
Hi, I am trying to run ANOVA with an interaction term on 2 factors (treat has 7
levels, group has 2 levels). I found the coefficient for the last interaction
term is always 0, see attached dataset and the code below:
> test<-read.table("test.txt",sep='\t',header=T,row.names=NULL)
> lm(y~factor(t
imable?
Thanks
John
From: David Winsemius
Cc: "r-help@r-project.org"
Sent: Monday, November 7, 2011 5:13 PM
Subject: Re: [R] why NA coefficients
On Nov 7, 2011, at 7:33 PM, array chip wrote:
> Hi, I am trying to run ANOVA with an interaction term on 2 factors
>
> But why the coefficient for "treat 7-group 2" is not estimable?
>
> Thanks
>
> John
>
>
>
>
>
> From: David Winsemius
>
> Cc: "r-help@r-project.org"
> Sent: Monday, November 7, 2011 5:13 PM
> Subje
>> John
>>
>>
>> From: David Winsemius
>> Cc: "r-help@r-project.org"
>> Sent: Monday, November 7, 2011 5:13 PM
>> Subject: Re: [R] why NA coefficients
>>
>>
>> On Nov 7, 2011, at 7:33 PM, array chip wrote:
>>
>> &g
true, why it has to omit "treat 7-group 2"
Thanks again
From: David Winsemius
Cc: "r-help@r-project.org"
Sent: Monday, November 7, 2011 10:19 PM
Subject: Re: [R] why NA coefficients
On Nov 7, 2011, at 10:07 PM, array chip wrote:
reat 1 2
>> 1 8 0
>> 2 1 5
>> 3 5 5
>> 4 7 3
>> 5 7 4
>> 6 3 3
>> 7 8 2
>>
>> But why the coefficient for "treat 7-group 2" is not estimable?
>>
>> Thanks
>>
>> John
>>
>>
Hi all,Â
I was trying to use glht() from multcomp package to construct a contrast on
interaction term
in a linear model to do some comparisons. I am little uncertain on how to
construct contrasts on a 3-way interaction containing a continuous variable,
and hope someone can confirm what I did i
Hi, I have the same question as Jason on how to estimate the standard error and
construct CI around S_1(t) - S_2(t). From summary.survfit(obj), how can I
combine the 2 survival estimates and the associated standard errors, to get an
estimate of standard error for the difference / then calculate
Hi, I am wondering if it is possible to get an estimate of standard error of
the predicted posterior probability from LDA using lda() from MASS? Logistic
regression using glm() would generate a standard error for predicted
probability with se.fit=T argument in predict(), so would it make sense t
Hi, didn't hear any response yet. want to give it another try.. appreciate any
suggestions.
John
To: "r-help@r-project.org"
Sent: Wednesday, February 8, 2012 12:11 PM
Subject: [R] standard error for lda()
Hi, I am wondering if it is possible to get an estima
9, 2012 2:59 PM
Subject: Re: [R] standard error for lda()
On Feb 9, 2012, at 4:45 PM, array chip wrote:
> Hi, didn't hear any response yet. want to give it another try.. appreciate
> any suggestions.
>
My problem after reading this the first time was that I didn't agr
Hi, I am wondering if we can make prediction on a linear mixed model by lmer()
from lme4 package? Specifically I am fitting a very simple glmer() with
binomial family distribution, and want to see if I can get the predicted
probability like that in regular logistic regression?
fit<-glmer(y~x+(
Hi, I have a microarray dataset from Agilent chips. The data were really log
ratio between test samples and a universal reference RNA. Because of the nature
of log ratios, coefficient of variation (CV) doesn't really apply to this kind
of data due to the fact that mean of log ratio is very close
Thank you Peter.
John
From: Peter Langfelder
To: Bert Gunter
Sent: Tuesday, February 21, 2012 2:51 PM
Subject: Re: [R] "CV" for log normal data
>
> Good advice. But perhaps ?mad or some other perhaps robust plain old
> measure of spread?
The problem is n
Hi, what does a low R-square value from an ANCOVA model mean? For example, if
the R square from the model is about 0.2, does this mean the results should NOT
be trusted? I checked the residuals of the model, it looked fine...
Thanks for any suggestion.
John
[[alternative HTML version
dalgaard
Cc: "r-help@r-project.org"
Sent: Monday, May 7, 2012 11:07 PM
Subject: Re: [R] low R square value from ANCOVA model
On May 8, 2012, at 05:10 , array chip wrote:
> Hi, what does a low R-square value from an ANCOVA model mean? For example, if
> the R square from the mo
John
From: peter dalgaard
Cc: "r-help@r-project.org"
Sent: Monday, May 7, 2012 11:43 PM
Subject: Re: [R] low R square value from ANCOVA model
On May 8, 2012, at 08:34 , array chip wrote:
> Thank you Peter, so if I observe a significant coefficient, that sig
n on this argument?
Many thanks!
John
From: peter dalgaard
Cc: "r-help@r-project.org"
Sent: Monday, May 7, 2012 11:43 PM
Subject: Re: [R] low R square value from ANCOVA model
On May 8, 2012, at 08:34 , array chip wrote:
> Thank you Pe
Paul, thanks for your thoughts. blunt, not at all
If I understand correctly, it doesn't help anything to speculate whether there
might be additional variables existing or not. Given current variables in the
model, it's perfectly fine to draw conclusions based on significant
coefficients reg
Hi, I was reviewing a manuscript where a linear mixed model was used. The data
is simple: a response variable "y" was measured for each subject over 3 time
points (visit 1, 2 and 3) that were about a week apart between 2 visits. The
study is a non-drug study and one of the objectives was to eval
9 AM
Subject: Re: [R] a simple mixed model
On May 27, 2012, at 07:12 , array chip wrote:
> Hi, I was reviewing a manuscript where a linear mixed model was used. The
> data is simple: a response variable "y" was measured for each subject over 3
> time points (visit 1, 2 and
Hi, is there a function to calculate fractional ranks?
Thanks
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal,
Hi, I would like to rbind 2 data frames. They both some common column names,
but also some unique column names each, is there any simple function that rbind
these 2 data frames with filling NAs for those columns of unique names?
thanks
__
R-help@r-pro
Hi, I am just wondering if there is a test available for testing if a linear
fit of an independent variable in a Cox regression is enough? Thanks for any
suggestions.
John Zhang
[[elided Yahoo spam]]
AIL PROTECTED]> wrote:
> supclust
>
> On 11/9/07, array chip <[EMAIL PROTECTED]>
> wrote:
> > Hi is there a package for diagonal linear
> discriminant
> > analysis (diagonal LDA)?
> >
> > Thanks
> >
> > ___
Hi,
The code round(0.0002234,4) will return 2e-04, how can
I return 0.0002 instead? I want to print 0.0002
instead of 2e-04 for formating purpose.
thanks
Looking for last minute shopping deals?
Hi,
I am trying to test some contrasts, using glht() in
multcomp package on fixed effects in a linear mixed
model fitted with lme() in nlme package. The command I
used is:
## a simple randomized block design,
## type is fixed effect
## batch is random effect
## model with interaction
sqtest())
However, after looking at the examples from the help
page of contrast(), I still couldn't figure out how to
specify that comparison.
Thanks for any suggestions.
--- Dieter Menne <[EMAIL PROTECTED]> wrote:
> array chip yahoo.com> writes:
>
> (Real names
Hi, I have been trying glht() from multcomp package
and contrast() from contrast package to test a
contrast that I am interested in.
With the following simulated dataset (fixed effect
"type" with 3 levels (b, m, t), and random effect
"batch" of 4 levels, a randomized block design with
interaction
Hi, I am running a simple one-way ANOVA with an
independent factot variable "treat" (3 levels: a, b
and c) and a response variable "y". I want to test a
linear relationship of the response among the 3 levels
of the variable "treat" (ordered a->b->c). I used
glht() from multcomp package. Later I fou
f a linear trend
> 3) is there a quadratic response
>
> If you declare your factor to be "ordered" then the
> default contrasts
> will be poly()nomials.
>
> Ross Darnell
>
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PRO
Hi I am using forestplot() in rmeta package on a
dataset of 45 point estimates with corresponding
confidence intervals. The resulting plot was just too
large and plotted out of the graphic window that I can
not see whole picture. Is there anyway to fix this
problem?
Thanks
___
Hi, it seems that the fastbw() in the Design package
only works with variable of class "factor" according
to the help page if I understand correctly. Is there
any R function/package that do stepwise variable
selection for a Cox model with continuous independent
variables?
Thank you
John
Rob Tibshirani propose to use lasso with Cox
regression for variable selection in his 1997 paper
"The lasso method for variable selection in the Cox
model" published in Statistics In Medicine 16:385. I
understand the lars() function in lars package
implemented lasso, but it does not do lasso with C
Hi,
When I install new packages from CRAN, I frequently
find that some packages were missing from the download
queue. For example, on one of my computer with R2.6.2,
I can not find package glmpath from the download
queue. On my other computer with R2.5.1, I could still
find that particular package
Hi,
I am new to model selection by coefficient shrinkage
method such as lasso. And I became particularly
interested in variable selection in Cox regression by
lasso. I became aware of the coxpath() in R package
glmpath does lasso on Cox model. I have tried the
sample script on the help page of cox
Hi, I am wondering how can I add a common title to the
top of a page that contains multiple plots using,
e.g., par(mfrow=c(2,3))?
thanks
John Zhang
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the pos
title', outer=T, line=-1)
>
> HTH
>
> Peter Alspach
>
>
> > -Original Message-
> > From: [EMAIL PROTECTED]
> > [mailto:[EMAIL PROTECTED] On Behalf Of
> array chip
> > Sent: Wednesday, 5 March 2008 10:48 a.m.
> > To: [EMAIL PROTECTED]
Hi, I have been playing with graphic parameters to
meet my specific plot requirement. I would like to
draw a plot in the top right region of the plot
region, I can do that with a number of parameters such
as plt, mar or oma. For example setting the
parameters:
par(plt=c(0.28,0.956,0.25,0.9))
or
pa
Hi is there a package for diagonal linear discriminant
analysis (diagonal LDA)?
Thanks
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and pro
Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (2 genes
x 550 samples) with survival endpoint. It quickly give the following error:
> library(samr)Loading required package: imputeLoading required package:
> matrixStats
Attaching package: ‘matrixStats’
The following objects
Sorry forgot to use plain text format, hope this time it works:
Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (2 genes
x 550 samples) with survival endpoint. It quickly give the following error:
> library(samr)
Loading required package: impute
Loading required package: m
Hi all,
The survdiff() from survival package has an argument "rho" that implements
Fleming-Harrington weighted long rank test.
But according to several sources including "survminer" package
(https://cran.r-project.org/web/packages/survminer/vignettes/Specifiying_weights_in_log-rank_comparison
Thank you David!
On Wednesday, February 14, 2018, 6:05:46 PM PST, David Winsemius
wrote:
> On Feb 14, 2018, at 5:26 PM, David Winsemius wrote:
>
>>
>> On Feb 13, 2018, at 4:02 PM, array chip via R-help
>> wrote:
>>
>> Hi all,
>>
>
Thank you Terry. Right now I can use comp() from survMisc package to do the
2-parameter version of F-H weighting. I think both SAS and stata offer the
2-parameter version, so just thought it would be nice if survdiff() can have
that option given it's standard package in R.
Thanks!
John
On
Dear all, I am new to lattice, so would appreciate anyone's help on the
questions below. I am using xyplot to plot some trend in my dataset. Using the
example dataset attached, I am trying to plot variable "y" over variable "time"
for each subject "id":
dat<-read.table("dat.txt",sep='\t',header=
Thanks all for the clarification!
From: Jeff Newmiller
To: r-help@r-project.org; Bert Gunter ; array chip
Cc: "r-help@r-project.org"
Sent: Monday, May 1, 2017 10:53 AM
Subject: Re: [R] Lattice xyplot
It is not a question of whether lattice "understands&quo
Hi, I am running a logistic regression on a simple dataset (attached) using glm:
> dat<-read.table("dat.txt",sep='\t',header=T)
If I use summary() on a logistic model:
> summary(glm(y~x1*x2,dat,family='binomial'))
Coefficients: Estimate Std. Error z value Pr(>|z|)(Intercept)
19.57
Hi,
I am learning to use your gsDesign package! I have a question about Pocock and
OBF boundary. As far as Iunderstand, these 2 boundaries require equal spacing
between interim analyses(maybe this is not correct?). But I can still use
gsDesign to run an analysisbased on unequal spacing:
gsDes
her the above analysis is still valid? Or for
unequal spacing, I have to use Lan-Demet’s error spending function
approximations? Thank you,
From: Berend Hasselman
To: array chip
Cc: R-help Mailing List
Sent: Friday, September 22, 2017 11:46 PM
Subject: Re: [R] gsDesign Pocock & OBF b
] https://cran.r-project.org/web/packages/reprex/index.html (read the
vignette)
--
Sent from my phone. Please excuse my brevity.
On September 23, 2017 9:53:05 PM PDT, array chip via R-help
wrote:
>Sorry for messed up text. Here it goes again:
>I am learning to use the gsDesign package.
&
Hello,
Can anyone suggest a simple way to generate a Kaplan-Meier plot with 2 survfit
objects, just like this one:
https://drive.google.com/file/d/1fEcpdIdE2xYtA6LBQN9ck3JkL6-goabX/view?usp=sharing
Suppose I have 2 survfit objects: fit1 is for the curve on the left (survtime
has been truncate
new clipping rectangle will persist until you or
something else resets it.
Jim
On Tue, Sep 29, 2020 at 10:34 AM array chip via R-help
wrote:
>
> Hello,
>
> Can anyone suggest a simple way to generate a Kaplan-Meier plot with 2
> survfit objects, just like this one:
>
&g
0, 1, 0.2), labels = FALSE, lty = "dashed")
Regards,
Marc Schwartz
> On Sep 28, 2020, at 8:33 PM, array chip via R-help
> wrote:
>
> Hello,
>
> Can anyone suggest a simple way to generate a Kaplan-Meier plot with 2
> survfit objects, just like this one:
>
&
direct way would be:
plot(fit1, col=1:2)
xylim<-par("usr")
clip(4,xylim[2],xylim[3],xylim[4])
lines(fit2,col=1:2)
Remember that the new clipping rectangle will persist until you or
something else resets it.
Jim
On Tue, Sep 29, 2020 at 10:34 AM array chip via R-help
wrote:
>
&g
perate until you have issued a graphics command. Try:
points(-1,-1)
before calling lines()
Jim
On Wed, Sep 30, 2020 at 12:26 PM array chip wrote:
>
> Hi Jim,
>
> I tried the clip() function below, surprisingly it did not work! I read the R
> help file and feel your script should w
hics command. Try:
points(-1,-1)
before calling lines()
Jim
On Wed, Sep 30, 2020 at 12:26 PM array chip wrote:
>
> Hi Jim,
>
> I tried the clip() function below, surprisingly it did not work! I read the R
> help file and feel your script should work. To have a workable exampl
nes" method that resets the clipping
region out of sight. Fortunately Mark Schwartz provided a way to get
your plot so I will give the wall against which I have been banging my
head a break.
Jim
On Wed, Sep 30, 2020 at 1:57 PM array chip wrote:
>
> Jim,
>
> I tried a few things
ll against which I have been banging my
head a break.
Jim
On Wed, Sep 30, 2020 at 1:57 PM array chip wrote:
>
> Jim,
>
> I tried a few things, I found that clip() works if I just do some regular
> graphing tasks. But as long as I run lines(fit) with "fit" object is
4:41:57 PM PST, array chip via R-help
wrote:
>Dear all, I have this simple dataset to measure the yeild of a crop collected
>in 2 batches (attached). when I ran a simple inear mixed model using lmer to
>estimate within-batch and between-batch variability, the between-batch
>variabil
Hi,
I downloaded R4.0.2 and installed it succesffully without any error. However,
when I opened up a R session (using x64) and tried to install packages, I got
the following error message:
> utils:::menuInstallPkgs()
Warning: failed to download mirrors file (internet routines cannot be loaded);
PDT, array chip via R-help
wrote:
Hi,
I downloaded R4.0.2 and installed it succesffully without any error. However,
when I opened up a R session (using x64) and tried to install packages, I got
the following error message:
> utils:::menuInstallPkgs()
Warning: failed to download mirrors f
Hello everyone,
I saw this scatterplots from a paper and thought it looked very nice:
https://drive.google.com/file/d/1V7F1gq-J_GIFDOrJs00hwGyXUqCZ_xwa/view?usp=sharing
It was similar to stripchart() with 'jitter' method, but it has a special
pattern of aligning points which made it look nice
Hello everyone,
I saw this scatterplots from a paper and thought it looked very nice:
https://drive.google.com/file/d/1V7F1gq-J_GIFDOrJs00hwGyXUqCZ_xwa/view?usp=sharing
It was similar to stripchart() with 'jitter' method, but it has a special
pattern of aligning points which made it look nice
Hello,
I made a mistake today on simple counting in R, that almost got me into
trouble. After trying multiple times, I finally figured out it's rounding issue
in R.
For exmaple, when I just simply type:
> (6.9-6.3) > 0.6
[1] TRUE
6.9-6.3 should be 0.6 exactly, but R thinks that it's greater t
Thanks Richard. Got it now...
On Thursday, September 3, 2020, 10:12:36 PM PDT, Richard M. Heiberger
wrote:
FAQ 7.31
On Fri, Sep 4, 2020 at 12:47 AM array chip via R-help
wrote:
>
> Hello,
>
> I made a mistake today on simple counting in R, that almost got me into
> troubl
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